First rounds of tourney should be seed 1 vs. seed 2 in one half and 3 vs. 4 in other half. This ensures good tennis in the early going and also ensures that top players cannot avoid playing one another. This ensures Nadal plays Federer and if either wins a tourney, they would have to played each other.
You speak as if there are only two top players around. However much I like to see Feds play Rafa, I ensure you that there's more to tennis than just Those Two. The other players can play pretty well, too (ask Rafa for that matter
So I don't think this would be of any help.